No.613 (City of Manchester) Squadron had a very varied wartime career, beginning as an army cooperation squadron and flying coastal patrols, air-sea rescue missions, tactical reconnaissance and fighter-bomber missions before ending the war as a night intruder squadron.

The squadron was formed on 1 March 1939 as an army co-operation squadron in the Auxiliary Air Force. A shortage of aircraft meant it was originally equipped with the Hawker Hind bomber, and even when army co-operation aircraft did arrive late in 1939 it was in the form of the obsolete Hawker Hector. It was only in April 1940 that the squadron finally received the Westland Lysander. In the following month the German offensive in the west began, and the squadron used both its Lysanders and its Hectors. The first operation came on 26 May when both types were used in an attack on German field guns near Calais. The squadron was engaged in light bombing and supply drops until early June.

Late in June a detachment from the squadron began to fly dawn and dusk coastal patrols to guard against German invasion. The detachment was soon joined by the entire squadron and this duty was performed until November 1940.

During 1941 the squadron was used to support training, flying a mix of radar calibration, air firing training and gas spraying training as well as taking par tin army training.

In August 1941 the first Tomahawks arrived, and were used alongside the Lysanders into 1942. Mustangs began to arrive in June 1942, and by the end of the year the squadron had standardised on the new aircraft. On 5 December the squadron went operational with the Mustang, flying reconnaissance mission along the French coast. The squadron also took part in Rhubarbs, fighter sweeps across France.

Early in 1943 the squadron moved north to take part in army exercises. In April 1943 it moved to East Anglia and began to take part in Lagoons, anti-shipping strikes off the Dutch Coast. No.613's Mustangs operated alongside Beaufighters from Coastal Command. These operations continued into the summer of 1943. In the same period the squadron also flew on Instep missions, escorting Mosquitoes operating over the Bay of Biscay and in patrols over the Frisian Islands, searching for German minesweeping aircraft.

In October 1943 the squadron was withdrawn from operations and began to convert to the Mosquito. Fighter-bomber operations began in December 1943. These included at least one of the famous precision missions flow by Mosquito squadrons, when on 11 April 1944 Wing Commander R. N. Bateson led six aircraft in a raid on a five storey building in The Hague being used to store the principle register of the population of the city. The raid was a success, destroyed the records that were being used by the Gestapo to trace the local resistance.

In May 1944 the squadron began to fly night intruder missions. In November it moved to France, where it remained for the rest of the war. The squadron was renumbered as No.69 Squadron on 7 August 1945. A new 613 Squadron was formed in the Auxiliary Air Force in May 1946.